Bio 160 final exam study guide
Bio 160 final exam study guide Bio 160
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This 24 page Study Guide was uploaded by Christina Bouchillon on Wednesday May 4, 2016. The Study Guide belongs to Bio 160 at University of Tennessee - Knoxville taught by Dr. Madision in Spring 2016. Since its upload, it has received 59 views. For similar materials see Cellular and Molecular Biology in Biology at University of Tennessee - Knoxville.
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Date Created: 05/04/16
Final Exam Study Guide Definitions you should memorize • Hydrophilic interacting readily with water. Hydrophilic compounds are typically polar compounds containing partially or fully charged atoms. • Hydrophobic not readily interacting with water. Typically nonpolar compounds that lack partially or fully charged atoms • Cohesion tendency of certain like molecules to cling together due to attractive force • Adhesion tendency of certain dissimilar molecules to cling together due to attractive force • Surface tension cohesive force that causes molecules at the surface of a liquid to stick together • Solvent any liquid in which one or more solids or gases can dissolve • Solute any substance that is dissolved in a liquid • Enzyme a protein catalyst used by living organisms to speed up and control biological reactions • Catalyze To speed up or initiate a chemical reaction. (Catalysts do this) • Substrate The specific molecule acted upon by an enzyme. • Active site The location in the enzyme that substrate fits within. • Denatured destroy the characteristic properties of (a protein or other biological macromolecule) by heat, acidity, or other effects that disrupt its molecular conformation. • Molecular chaperones proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures • Ribozyme ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction. • Antiparallel parallel but moving or oriented in opposite directions (5’3’) (3’5’) • Complementary base pairing either of the nucleotide bases linked by a hydrogen bond on opposite strands of DNA or doublestranded RNA: guanine is the complementary base of cytosine, and adenine is the complementary base of thymine in DNA and of uracil in RNA (G+C)(A+T/U) • Template strand the sequence of DNA that is copied during the synthesis of RNA • Hypertonic comparative term designating a solution that, if inside a cell or vesicle, results in the uptake of water and swelling or even bursting of the membranebound structure. This solution has a greater solute concentration than the solution on the other side of the membrane. Used when the solute is unable to pass through the membrane. The cell is hypertonic, and the solution is hypotonic. • Hypotonic comparative term designating a solution that, if inside a cell or vesicle, results in the loss of water and shrinkage of the membranebound structure. This solution has a lower solute concentration than the solution on the other side of the membrane, used when the solute is unable to pass through the membrane. The cell is hypotonic, and the solution is hypertonic. • Isotonic comparative term designating a solution that, if inside a cell or vesicle, results in no net uptake or loss of water and thus no effect on the volume of the membranebound structure. This solution has the same solute concentration as the solution on the other side of the membrane. • Spontaneous reaction Reaction in which the reactants are of higher PE than its products, i.e. an increase in entropy. • Nonspontaneous reaction A reaction in which the products are of a higher PE than the reactants, i.e. an increase in enthalpy. • Exergonic Releases energy (a spontaneous reaction) • Endergonic Requires energy (nonspontaneous) • Chromosome Genecarrying structure consisting of a single long molecule of double stranded DNA and associated proteins (e.g., histones). Most prokaryotic cells contain a single, circular chromosome; eukaryotic cells contain multiple noncircular (linear) chromosomes located in the nucleus. • Sister chromatid The paired strands of a recently replicated chromosome, which are connected at the centromere and eventually separate during anaphase of mitosis and meiosis II. Compare with nonsister chromatids. • Homologous chromosomes In a diploid organism, chromosomes that are similar in size, shape, and gene content. Also called homologs. • Histones one of several positively charged (basic) proteins associated with DNA in the chromatin of eukaryotic cells • Nucleosome a repeating, beadlike unit of eukaryotic chromatin, consisting of about 200 nucleotides of DNA wrapped twice around eight histone proteins • Chromatin the complex of DNA and proteins, mainly histones, that composes eukaryotic chromosomes. Can be highly compacted (heterochromatin) or loosely collected (euchromotin) • Haploid Having one set of chromosomes (1n or n for short). (2) A cell or an individual organism with one set of chromosomes. • Diploid Having two sets of chromosomes (2n). (2) A cell or an individual organism with two sets of chromosomes, one set inherited from the mother and one set from the father. • Polyploid the state of having more than two full sets of chromosomes, either from the same species (autopolyploidy) or from different species (allopolyploidy) • Aneuploid The state of having an abnormal number of copies of a certain chromosome. • Ploidy The number of complete chromosome sets present. Haploid refers to a ploidy of 1; diploid, a ploidy of 2; triploid, a ploidy of 3; and tetraploid, a ploidy of 4. • Haploid number The number of different types of chromosomes in a cell. Symbolized as n. • Diploid number the number of chromosomes present in the body cells of a diploid organisms • Sex chromosomes Chromosomes that differ in shape or in number in males and females. For example, the X and Y chromosomes of many animals • Autosomes Any chromosome other than a sex chromosome (i.e,. any chromosome other than the X or Y in mammals). • Gene A section of DNA (or RNA, for some viruses) that encodes information for building one or more related polypeptides or functional RNA molecules along with the regulatory sequences required for its transcription. • Allele a particular version of a gene • Nonsister chromatids The chromatids of a particular type of chromosome (after replication) with respect to the chromatids of its homologous chromosome. Crossing over occurs between nonsister chromatids. Compare with sister chromatids. • Fertilization fusion of the nuclei of two haploid gametes to form a zygote with a diploid nucleus • Zygote the cell formed by the union of two gametes; a fertilized egg • Crossing over The exchange of segments of nonsister chromatids between a pair of homologous chromosomes that occurs during meiosis I. • Nondisjunction An error that can occur during meiosis or mitosis, in which one daughter cell receives two copies of a particular chromosome and the other daughter cell receives none. • Dominant allele Referring to an allele that determines the same phenotype when it is present in homozygous or heterozygous form.. Compare with recessive. • Recessive allele Referring to an allele whose phenotypic effect is observed only in homozygous individuals. Compare with dominant. • Homozygous Having two identical alleles of a gene. • Heterozygous Having two different alleles of a gene. • Genotype All the alleles of every gene present in a given individual. Often specified only for the alleles of a particular set of genes under study. Compare with phenotype. • Phenotype The detectable traits of an individual. Compare with genotype. • Linked genes means that the genes are located on the same chromosome and inherited together. • DNA polymerase There are three versions of the enzyme DNA Polymerase, labeled I, II and III. DNA Pol III is the specific enzyme responsible for creating new DNA strands during DNA replication. • gene An allele or set of alleles that determine heredity. • mRNA Messenger RNA, assembled in the nucleus (process of splicing + capping) and sent out to ribosomes where they join with tRNA (transferRNA) to translate nucleic acid codons into proteins. • transcription Transfer of information from DNA to RNA same “language” of nuclei acids • translation transfer of info from RNA to different “language” of proteins • genetic code series of codons in a gene • triplet code AKA a codon, any given set of three nitrogenous bases e.g. AUG • codon see above • reading frame the reading frame determines which triplets will become discrete codons, e.g. AGTTGCACTGG can be read as “AGTTGCACT” or “TTGCACTGG”. A frame shift mutation will, by adding or deleting a base, cause the frame to shift and the codons to become completely mistranslated. Can someone explain this more??? • start codon AUG codes for methionine, the start codon. • stop codon UAA, UAG, and UGA are stop codons, signaling the end of the translated amino acid. • mutation an alteration of DNA. • point mutation the mutation of a single nitrogenous base. • missense mutation a point mutation that causes the translation of a different amino acid. • nonsense mutation a point mutation that changes a codon’s amino acid into a stop codon. • silent mutation Many codons code for the same amino acid. A silent mutation is when a codon’s triplet set is changed, but it still codes for the same amino acid. A type of neutral mutation. • frameshift mutation A mutation that adds or deletes a nitrogenous base, resulting in a shift of the reading frame. • beneficial mutation a mutation that inadvertently increases the individual’s fitness. • neutral mutation a mutation that does not affect the individual’s fitness. • deleterious mutation a mutation that harms the fitness of the individual. • chromosome mutations (inversion, translocation, deletion, duplication) a missing, extra, or irregular portion of chromosomal DNA. It can be from an atypical number of chromosomes or a structural abnormality in one or more chromosomes Inversion a chromosome rearrangement in which a segment of a chromosome is reversed end to end. Translocation rearrangement of parts between nonhomologous chromosomes. Deletion part of a chromosome or a sequence of DNA is lost during DNA replication. Duplication a portion of a genetic material or a chromosome is duplicated or replicated, resulting in multiple copies of that region. • RNA polymerase Enzyme that transcripts RNA from DNA. • sigma Sigma factors are subunits of the DNAdependent RNA polymerase holoenzyme (RNAP). It is a protein needed ONLY for initiation of RNA synthesis. • core enzyme Consists of the subunits of an enzyme needed for catalytic activity. • holoenzyme a biochemically active compound formed by the combination of an enzyme with a coenzyme. • downstream Relative term, indicating that the gene/allele/codon described as “downstream” is more towards the 3’ end (remember, DNA is 5’ to 3’). • upstream Opposite of downstream • promoter a region of DNA that initiates transcription of a particular gene. • TATA box a DNA sequence indicating where a gene sequence can be read and decoded. A type of promoter sequence, it signals to RNAP where transcription begins. It is named for its conserved DNA sequence, most commonly TATAAA. Many eukaryotic genes have a TATA box 2535 base pairs upstream of the transcription start site. • transcription factors A protein that binds to DNA and regulates gene expression by promoting or suppressing transcription. Binds either to enhancer or promoter regions of DNA, using a variety of mechanisms to control gene expression. They can stabilize or block RNAP DNA binding, catalyze acetylation or deacetylation of histones (changing the shape of the chromosomes for access) or recruit coactivators/corepressor proteins. • poly(A) signal An RNA code that acts as a signal to the RNA cleavage complex to begin splicing and polyadenylation, 1030 bases downstream of its binding site. • primary transcript singlestranded RNA product produced by transcription and processed to yield mRNA, tRNA, rRNA, etc. • premRNA Precursor to messenger RNA, but it hasn’t been spliced and capped yet. • exons codons in premRNA that are not removed by splicing. • introns Codons in premRNA that are removed by splicing. • splicing Process of removing introns from premRNA. An enzyme brings introns together and “snips” them off, joining exons to exons. • snRNPs Small Nuclear RiboNucleoProteins. RNAprotein complexes that combine with unmodified premRNA and others to form a spliceosome, a vital splicing component of mRNA processing. • spliceosome Enzyme that splices premRNA into mRNA, made of snRNPs and pre mRNA. • 5’ cap a specially altered nucleotide, attached to the 5’ end of mRNA, consisting of a Guanine connected by an unusual 5’ to 5’ triphosphate linkage. This regulates export, prevents degradation, promotes translation and promotes intron excision. • poly(A) tail A process called polyadenylation adds a poly(A) tail to a premRNA in the process of capping which helps it to become a fullfledged mRNA. It’s literally a chain of RNA that has only adenine bases, also called adenosine monophosphates. It’s important for the export, translation and stability of mRNA. It shortens over time and eventually, when it gets too short, the mRNA is enzymatically degraded or stored for later activation. • RNA processing Splicing and capping, creating mRNA from premRNA. • polyribosome a multiribosome complex capable of building massively complex organic molecules. • tRNA transfer RNA that brings amino acid residues to a ribosome joined with mRNA, important to amino acid synthesis • anticodon the triplet codons in tRNA that complement the codons in mRNA. • aminoacyltRNA synthetases An enzyme that attaches the appropriate amino acid onto its tRNA. This is sometimes called charging or loading the tRNA with the amino acid. Once it’s charged, a ribosome transfers the amino acid from the tRNA onto the growing peptide. Important to translation. • aminoacyl tRNA A type of RNA usually called aatRNA or charged tRNA. This is a tRNA that has an amino acid loaded by aminoacyltRNA synthetase. • rRNA The ribosomal RNA is the RNA component of the ribosome. Essential for protein synthesis in all living or ganisms. • translocation chromosome abnormality caused by rearrangement of parts between NONhomologous chromosomes. Occurs when a piece of one chromosome “breaks off and sticks” to another chromosome. • elongation factors set of proteins used in protein synthesis. In the ribosome, they facilitate translational elongation. They add amino acids to the growing peptide chain at about 1520 per second (in prokaryotes) and about two per second (eukaryotes). • release factor protein factor allowing for the termination of translation by recognizing the stop codon in mRNA. • molecular chaperones proteins that assist the covalent folding or unfolding, or the assembly/disassembly, of macromolecular structures. • 5’ UTR a UTR is an UnTranslated Region of RNA. The 5’ UTR, at the “front” of mRNA, is sometimes called the leader sequence or leader RNA. It is directly upstream from the initiation codon (AUG) and is important for regulating translation of a transcript. According to the review notes, all we need to know about UTRs is that they regulate translation. • 3’ UTR Section of UnTranslated mRNA that immediately follows the stop codon during translation. • gene expression The physical expression of a specific allele or set of alleles. • transcriptional control control of gene expression that occurs at transcription. This is the first step of possible control. For example, the process of unraveling histones to expose sections for transcription, the lac operon which prevents transcription in the presence of glucose, etc. • translational control control of gene expression that occurs at translation, most often at initiation of translation. For example, elevated levels of growth factors can trigger translation. Another example is recognizing the stop codon and ceasing translation. • posttranslation control Control of gene expression that occurs after translation of the PROTEIN. This can be done by phosphorylation, lipidation, peptide bond cleaving, etc. etc. • constitutively A constitutively active protein is a protein which is constantly active. • constitutive mutant A mutant organism that continuously produces a protein (possibly in excess) due to a mutated regulatory gene, which is always expressed or impossible to turn off. An E. coli bacterium with a mutated lac operon would be a constitutive mutant, constantly producing proteins to metabolize lactose. • inducer a molecule that regulates gene expression. It can bind to repressors (disabling them) or activators. • repressor a DNA or RNAbinding protein that inhibits gene expression by binding to either an operator or a silencer. DNAbinding repressors physically block RNA Pol. attachment, preventing transcription. • activator A transcriptional activator is a protein that increases or activates gene transcription. • operon A functional genomic DNA unit consisting of a cluster of genes under the control of a single promoter. • operator a segment of DNA which binds to a transcription factor (a repressor) to regulate gene expression. • regulon A group of genes that are regulated as a unit, generally by the same regulatory gene. • negative control Does she mean negative feedback control here? A negative control is a type of control group in a scientific experiment. A negative feedback control is when a process creates products that are sensed by the organs responsible for the process, indicating to them that the process should cease. An example would be gland X releasing hormone X which stimulates cells to release hormone Y. When there is an excess of Y, gland X senses this and stops producing hormone X. definition from book, negative control: Of genes, when a regulatory protein shuts down expression by binding to DNA on or near the gene. • positive control “A produces B which in turn produces more of A”.For example, a gene activating itself directly or indirectly via a double negative feedback loop. The lac operon in E. coli is an example of this. Definition from book, positive control: Of genes, when a regulatory protein triggers expression by binding to DNA on or near the gene. • allosteric regulation The regulation of an enzyme by binding an effector molecule at a site OTHER than the enzyme’s active site, changing the shape and rendering it unusable. • differential gene expression Every cell in our bodies has the same DNA, so each allele is expressed or not, depending on cell function, through a series of processes. • chromatin the complex of DNA and proteins, mainly histones, that composes eukaryotic chromosomes. Can be highly compacted (heterochromatin) or loosy collected (euchromatin) • chromatin remodeling The process of altering the quaternary structure of chromatin, compacting or loosening it to expose different genes for transcription. • histones one of several positively charged (basic) proteins associated with DNA in the chromatin of eukaryotic cells • nucleosome a repeating, beadlike unit of eukaryotic chromatin, consisting of about 200 nucleotides of DNA wrapped twice around eight histone proteins. • DNA methyltransferases Enzymes that transfer a Methyl group (A single carbon and its attached hydrogens, CH3) to a nucleotide, which is an epigenetic mechanism used to control gene expression. • histone acetyltransferases Enzymes that transfer an acetyl group to a histone, changing its charges and causing it to unravel or change shape. • histone deacetylases Histones that remove an acetyl group. • chromatinremodeling complexes Chromatin remodeling is the “dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription proteins”. A protein complex that catalyzes removal or addition of methyl or acetyl or whatever groups is a chromatinremodeling complex. • epigenetic inheritance Transmittance of information from one generation to the next (parent to a child) that affects the offspring’s traits without altering the primary DNA structure. • promoter region of DNA that initiates transcription of a particular gene, upstream of the gene. • enhancers a short region of DNA that can be bound to by activators to activate transcription. • silencers A DNA sequence capable of binding repressors. • repressors a transcription regulation factor that blocks gene expression by binding to the operator or silencer. • transcriptional activators a protein that increases gene transcription of a gene or genes. • alternative splicing A single gene codes for multiple proteins, by changing which exons are allowed through the splicing process. • RNA interference the process of RNA molecules inhibiting gene expression, usually by destroying specific mRNA molecules. microRNA (mirNA) and small interfering RNA (siRNA) are central to RNA interference. These can bind to mRNA and restrict or promote their activity. This is a type of posttranscription control. • proteasome protein complexes in all eukarya and archaea, and in some bacteria. The main purpose is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Things you should be able to do • Explain the five big ideas of biology (FBIs) and how they relate to what we have learned Structure affects function, Information flow and storage, Transformation of matter and energy, Evolution, Systems I came up with a mnemonic device to remember them. Stinky Elephants Stand In Trees Structure, Evolution, Systems, Information, Transformation. • Describe the 5 fundamental characteristics of life and use these characteristics to determine if something is alive 1. Capable of replication, 2. process Info, 3. made up of one or more cells, 4. product of evolution, 5. acquire and use energy • Distinguish between ionic, nonpolar covalent, polar covalent, and hydrogen bonds Ionic bond chemical bond that is formed when an electron is completely transferred from one atom to another so that the atoms remain associated due to their opposite electric charges. Note: Ionic bonds ALWAYS include a metal and a nonmetal, e.g. KI, NaCl, etc. Covalent bond type of chemical bond in which two atoms share one or more pairs of electrons. ALWAYS only consists of nonmetals, e.g. CO2, H2O Nonpolar covalent bond a type of chemical bond in which two atoms share one or more pairs of electrons evenly. Polar covalent bonda type of chemical bond in which two atoms share one or more pairs of electrons unevenly, exhibiting a net dipole moment. Hydrogen bondweak interaction between two molecules or different parts of the same molecule resulting from the attraction between a hydrogen atom with a partial positive charge and another atom (usually F, O, or N) with a partial negative charge • Explain how the ability of water to form hydrogen bonds gives it many of its life supporting properties Common solvent Relatively high melting and boiling point temperatures; more energy is required to break the hydrogen bonds between water molecules Water molecules stay close to each other (cohesion), due to the collective action of hydrogen bonds between water molecules Water also has high adhesion properties because of its polar nature. Example: On extremely clean/smooth glass the water may form a thin film because the molecular forces between glass and water molecules (adhesive forces) are stronger than the cohesive forces. Water also has high surface tension because the strong Hydrogen bonds at the surface are resistant to penetration. Water’s hydrogen bonds create a highvolume lattice when frozen, making ice float above water which prevents lakes from freezing solid. • List the monomers for carbohydrates, nucleic acids, and proteins carbohydrates: monosaccharides nucleic acids: nucleotides proteins: amino acids Remember: Lipids do not have true monomers. • List examples of carbohydrates, lipids, nucleic acids, and proteins carbohydrates: corn lipids: cheese, milk, butter proteins: • Identify the images of a protein, a nucleic acid, a carbohydrate, and a lipid Proteins are chains of amino acid sequences. Nucleic acids are easy remember the DNA diagrams we did on an exam. Cyclic sugar, nitrogenous base, phosphate group. Lipids are usually hydrocarbon chains, with “heads” and “tails”. • List the four key differences between prokaryotic and eukaryotic cells • Compare and contrast plant cells and animal cells Plants: cell wall, chloroplast, crowded with organelles, vacuoles Animal: centrioles, lysosome, lots of space inside between organelles Both: nucleus, rough ER, smooth ER, ribosomes, golgi apparatus, peroxisome, mitochondrion, plasma membrane, cytoskeletal element • Compare and contrast the structures and functions of the following components: peroxisomes, rough ER, smooth ER, Golgi apparatus, lysosomes, vacuoles, nucleus, ribosomes, chloroplasts, mitochondria, cytoskeleton, plasma membrane, and cell wall • Explain how an enzyme’s active site can reduce the activation energy of a reaction Remember induced fit. Enzyme changes the shape of the substrate at the active site to maximize reactivity. • Explain the overall equation for cellular respiration C 6 12 +66O → 62O + 6H O2 Heat2 Glucose is combusted by oxygen in order to produce carbon dioxide (emitted as waste), water (used to replenish the electron transport chain) and heat (released as chemical energy). • Compare the reactants, products, and energy yield of aerobic metabolism versus lactic acid fermentation and alcohol fermentation Aerobic metabolism is by far the most efficient because it uses O as the FINAL electron acceptor in the ETC, creating a more potent electrochemical gradient that allows oxidative phosphorylation. Meanwhile lactic acid fermentation is used in the absence of oxygen (which shuts down the ETC preventing NADH from reducing the next molecule). The pyruvate from glycolysis instead accepts these electrons, regenerating NAD+ (KEY POINT) and forming lactate (this acts as the final electron acceptor), a form of lactic acid. This is much less efficient. Why does this happen? → it happens to produce minimal ATP by regenerating Glucose. Lactose is converted back to glucose in the liver!! 2 net ATPs can then be created in another cycle of glycolysis. Finally there is alcohol fermentation, where instead of donating NADH electrons to pyruvate, yeast converts pyruvate to the twocarbon acetaldehyde, giving off CO2 which makes bread rise and champagne bubble. Acetaldehyde accepts NADH electrons, forming NAD+ required for glycolysis. This forms ethanol, a waste product. Compare the location in the cell (in eukaryotes and prokaryotes), and energy yield of the following stages of cellular respiration (glycolysis, pyruvate processing, citric acid cycle, and electron transport and oxidative phosphorylation) 1.Glycolysis: occurs in cytoplasm. inputs: glucose, 2 ATP, 4 ADP, 2 NAD+ outputs: 2 pyruvate, 4 ATP, 2 ADP, 2 NADH (2 Net ATP) 2.Pyruvate Processing: occurs in mitochondrial matrix inputs: 2 pyruvate, 2 NAD+, 2 CoA outputs: 2 CO2, 2 NADH, 2 Acetyl CoA 3.Citric Acid Cycle: occurs in mitochondrial matrix (eu), cytoplasm (pro) inputs: 6 NAD+, 2 FAD, 2 Acetyl CoA, 2 ADP outputs:6 NADH, 2 FADH2, 2 CoA, 2 ATP, 4 CO2 → this is for when a molecule of glucose is broken down and goes through the cycle twice. If only one cycle occurs with one acetyl CoA, 1ATP (or GTP) is produced, 3 NADH, 1 FADH2, and 2 CO2. 4.electron transport chain: occurs in mitochondrial inner membrane (eu), plasma membrane (pro) inputs: 10 NADH, 25 ADP, 2 FADH2, 6 O2 outputs: 10 NAD+, 25 ATP, 2 FAD, 6 H2O ∙ Electrons go to molecular oxygen, and then the oxygen is REDUCED to water as the final step of the ETC ∙ NADH and FADH2 are electron carriers ∙ Four Complexes in ETC then goes to ATP synthase ^^^ most energy • Explain why photosynthesis is important to all living organisms Plants convert solar energy into chemical energy which is then channeled up through the food chain. • Explain why leaves are green with reference to the electromagnetic spectrum Leaves are green because of the pigments embedded in the thylakoid membrane. This pigment absorbs light of all visible (and some invisible) wavelengths EXCEPT green, which it reflects. This is why plants are green. • Explain the overall equation for photosynthesis in plants Sunlight + 6 CO2 + 6 H20 = Glucose + 6 O2 Sunlight is used to excite electrons that power an ETC and create an electrochemical gradient. Protons are pumped into the chloroplast and then back through, passing through ATP Synthase. This creates ATP energy and releases O2 as waste. CO2 is fixed from the atmosphere during the Calvin cycle, which utilizes ATP to create glucose which is used for energy and growth. • Compare meiosis and mitosis • Explain how defects in cell cycle regulation leads to cancer Cancers arise from cells in which cellcycle checkpoints have failed. There are 2 types of defects that relate to cell division: 1.) defects that makes the proteins required for cell growth active when they shouldn’t be and 2.)defects that prevent tumor suppressor genes from shutting down the cell cycle. • Explain how genetic variation arises from meiosis and fertilization meiosis results in the formation of gametes. During meiosis, crossing over occur that is the exchange of genetic material between the homologous chromosomes. This will lead to variation since the alleles separate during anaphase 1. independent assortment of chromosomes Chromosome can sort differently and exchange different amounts of information. It's a little complicated, but basically chromosomes can line up so that the replicates which were formed during meiosis can get multiple allele configurations. Example: Four chromosomes, two homologous pairs replicate. One from each pair has either recessive or dominant alleles. You can end up with either a recessiverecessive and dominantdominant, or both heterozygous. The sources has a link to help understand more. 2. crossing over during crossing over with gamete formation, genetic material from the mother (eggs) or father (sperm) are not all the same. You may get different combinations of traits from the father or mother. In other words, since a gamete is technically half the DNA from the father, the same half is not always taken from the father's genome. Synapsis occurs at the chiasma which is the little overlap of the two homologous chromosomes in meiosis I, this crossing over creates the tetrad shape thing at the beginning of meiosis (XX) 3. random fertilization Sperm all have different combinations of the father's DNA due to crossing over. Mix that up with the eggs from the mother which also contain different parts of her DNA, and you have a random chance that a particular sperm with particular traits is going to fertilize a particular egg with a particular trait. In other words, it's hard to get the exact same genes twice when having kids. • Define and distinguish between complete dominance, incomplete dominance, and codominance • Calculate probabilities of genotypes and phenotypes from a particular cross EX: AaBb x AaBb = 9:3:3:1 AaBb x aabb = 1:1:1:1 • Determine genotypic and phenotypic ratios from a particular cross • Write a sequence of doublestranded DNA that is 10 base pairs long, separate the strands, and without comparing them, write in the bases that are added during DNA replication • Draw and label a diagram of a replication bubble that shows (1) 5’ à 3’ polarity of the two parental DNA strands and (2) the leading and lagging daughter strands at each replication fork • Explain the logical connections between failure of repair systems, increases in mutation rate, and high likelihood of cancerdeveloping Repair systems fix mutations and prevent cells from dividing if they are unfit; this is carried out during the checkpoints of the cell cycle. If a repair system is mutated or fails, chances of mutations and cancers will increase. • Explain the central dogma of biology DNA > Transcription > RNA > Translation > Proteins • Explain how a compound that blocks RNA synthesis will affect protein synthesis • Explain where in a cell transcription and translation occur in eukaryotes and prokaryotes Eukaryotes transcription occurs in nucleus and translation in the cytoplasm. Prokaryotes transcription and translation occur in the cytoplasm • Describe how a change in the base sequence of a gene can result in a change in the phenotype of an organism changed codon creates different amino acid, altering cell function • Describe exceptions to the central dogma Genes that code for RNA molecules that are not translated into proteins, reverse transcriptase • Explain how the genetic code is redundant, unambiguous, nonoverlapping, nearly universal, and conservative Genes are redundant because many different codons code for the same amino acid. Genes are unambiguous because each specific codon codes for a single amino acid, never anything else. Genes are nonoverlapping because codons are read in a reading frame, so AGTGAT is AGT GAT, not AGTTGAGAT (which would be overlapping). Genes are nearly universal because in the vast majority of known organisms, a codon codes for the same amino acid. That is to say, mollusks, humans and dinosaurs all have methionine coded for by the codon AUG. Finally, genes are conservative because the genetic code is biased toward conservative amino acid mutations, a way of attempting to ensure that a given mutation will be silent or neutral. • Transcribe a DNA sequence into an mRNA sequence and then translate that mRNA sequence into an amino acid sequence (genetic code chart will be provided) • Explain how redundancy in the genetic code allows for silent mutations and whether a silent mutation is likely to be beneficial, neutral, or harmful Proline is a great example. If CCU becomes CCC, CCA, or CCG through a point mutation, the codon still creates proline. Many codons are arranged like this, to compensate for possible mutations and make them as impotent as possible. Silent mutations tend to be neutral. • Describe in detail the process of transcription (initiation, elongation, termination) in bacteria: ● Initiation: Small subunit binds to the mRNA, containing sites EPA. tRNA will approach at the P site, the large subunit will bind to the top. The first tRNA will have fMET or MET, the first for bacteria and the second for eukaryotes. ● Elongation: Many tRNAs are in the cytoplasm, but only ones that have the anticodons for the codons will stay. Peptidebond formation is created in the large subunit of the ribosome, and the first tRNA will encounter a second tRNA, which contains the next anticodon. Once that amino acid has been created, a bond forms between the two. Then, breaking off will occur with the first tRNA (which contains the first amino acid), and the first amino acid and the second amino acid will be joined, and the first tRNA will leave. Ribosomal translocation occurs when the ribosome will move towards the 3’ end of the DNA, moving towards the next codon. This will shift all the tRNA bound to the mRNA over a triplet, allowing the growing peptide to increase in length and continue growth. This uses aminoacyltRNA synthetases, the enzyme which causes the amino acid to rebind to the tRNA (as it has lost one, thus “recharging” the tRNA with another amino acid). ● In termination, a release factor binds to the A position (located in the small ribosomal subunit), which signals for the release of the ribosome from the mRNA. The finished polypeptide then folds properly and prepares for activation in a cell. • Compare transcription in bacteria and eukaryotes Bacteria do not splice and cap RNA. It is not exported because they have no nucleus. Also, instead of being stored in nuclear chromatin, DNA is often stored in plasmid form. • Explain why ribonucleoside triphosphates, rather than ribonucleoside monophosphates, are the monomers required for RNA synthesis A triphosphate molecule will have far more potential energy owing to the three negatively charged phosphates. • Describe the process of RNA splicing A spliceosome is created from a snRNP combining with a premRNA molecule, where it excises introns (superfluous or unimportant “junk” DNA) from the final transcripted product. Exons are preserved. • Explain the function of the 5’ cap and the poly(A) tail Molecular stability and facilitation of export and translation. • Describe the roles of the 5’ and 3’ UTRs They are important in regulating translation as well as the termination of translation. • Explain why the E, P, and A sites in the ribosome are appropriately named The A site is known as the Aminoacyl, appropriately named due to it being an ARRIVAL site. P is where peptidebond formation occurs. In bacteria, fMET attaches first. In eukaryotes, it should just attach a MET. E stands for exit, where the tRNA leaves. • Provide examples of posttranslational modifications direct control of the protein through enzymatic degradation or peptide excision. • Describe examples of transcriptional control, translational control, and post translational control and also explain which type of control provides the most rapid response and which type of control saves the most energy for the cell Posttranslational costs the most but is the most rapid response. Transcriptional control saves the most energy but takes the longest. Translational is in the middle. • Propose a strategy to isolate E. coli mutants with particular defect ???????? • Diagram the lac operon, showing the relative positions of the operator, the promoter, and the three protein coding genes; indicate what is happening at the operon in the absence and presence of lactose • Describe the function of lacZ, lacY, operator, promoter, repressor, lactose, and glucose in regulating lactose use in E. coli and predict the effect of mutations in each component l operon in E. coli Function to produce enzymes which break down lactose (milk sugar) lactose is not a common sugar, so there is not a great need for these enzymes when lactose is present, they turn on and produce enzymes Two components repressor genes and functional genes Three functional genes: lacZ produces Bgalactosidase. This enzyme hydrolyzes the bond between the two sugars, glucose and galactose lacY produces permease. This enzyme spans the cell membrane and brings lactose into the cell from the outside environment. The membrane is otherwise essentially impermeable to lactose. lacA produces Bgalactosidase transacetylase. The function of this enzyme is still not known, and is ignored in your book Promoter (P) aids in RNA polymerase binding Operator (O) "on/off" switch binding site for the repressor protein Repressor (lacI) gene Repressor gene (lacI) produces repressor protein w/ two binding sites, one for the operator and one for lactose The repressor protein is under allosteric control when not bound to lactose, the repressor protein can bind to the operator When lactose is present, an isomer of lactose, allolactose, will also be present in small amounts. Allolactose binds to the allosteric site and changes the conformation of the repressor protein so that it is no longer capable of binding to the operator • Explain how the ara operon functions Repression The ara operon is regulated by the AraC protein. If arabinose is absent, the dimer AraC protein represses the structural gene by binding to araI and araO1 and the DN2 forms a loop. The loop prevents RNA polymerase from binding to the promoter of the ara operon, thereby blocking transcription. • List a few examples of regulons The heat shock response in E. coli is regulated by sigma factor 32, whose regulon has been found to contain at least 89 open reading frames. • Explain how gene expression can be regulated in eukaryotes at six different levels (chromatin remodeling, transcription, RNA processing, mRNA stability, translation, post translational modification) ● Chromatin remodeling: this is DNA methylation or acetylation. DNA has an overall negative charge. When chromatin is condensed, it is unable to be transcribed. When acetyl groups are added onto histones, adding more negative charges, the DNA becomes looser, as the negative charges repel each other. These acetyl groups are added by HAT. HDAC removes the acetyl groups, making the chromatin condensed (regulates gene expression). ● Adding CH3 to DNA tends to have it be the condensed form (methylation). There are cases in which this can go either way. More methylation causes those genes to have a lower transcription rate. • Explain how certain patterns of histone acetylation or DNA methylation could influence whether a cell becomes a muscle cell or a brain cell Histone acetylation opens up access to condensed chromatin so it can be transcripted and genes may be expressed. DNA Methylation can activate or deactivate a specific DNA monomer. Both of these processes control gene expression, which is what determines a cell’s function as a muscle or brain cell. • Explain why the presence of certain transcription factors could influence whether a cell becomes a muscle cell or a brain cell certain regulatory proteins decondense chromatin at muscle or brain specific genes and then activate or repress the transcription of celltypespecific genesmusclespecific genes are expressed only if musclespecific regulatory proteins are produced and activated • Explain why the discovery or alternative splicing forced biologists to change their definition of a gene Alternative splicing affects which sets of genes are transcribed in different cell types, meaning a gene can code for more than one type of peptide. • Describe how microRNAs are produced and how they regulate gene expression MicroRNAs are a segment of DNA that is transcribed, producing a double stranded (hairpin loop?), premiRNA. It is processed to be only nineteen to twentyfour bases long, which is miRNA. This binds to RISC; one of the strands acts as a probe to find a target mRNA that is complementary to it. RISC cleaves the mRNA, which leads to degradation of the mRNA. This is used to degrade mRNAs. This is known as RNA interference, and it occurs in the cytoplasm. • Compare prokaryotic and eukaryotic gene expression and regulation of gene expression EUKARYOTES PROKARYOTES Similarities/differences in gene regulation • Explain how p53 is related to DNA damage, cell cycle arrest, apoptosis, DNA damage repair, and cancer ● P53 is a protein that activates when DNA damage is created. When mutations are sensed, the p53 gene will create proteins that arrest the cell cycle to prevent the mutation from spreading (replicating). During growth arrest, p53 activates transcription proteins involved in DNA repair. Without growth arrest, this leads to apoptosis in the cells when too many mutations accumulate. When these mutations continue to proliferate without a stop in the cell cycle, it leads to uncontrolled growth which will lead to cancer. It binds to an enhancer (a particular sequence). REVIEW SESSION IN NBA 118 NOTES ● Cellular Respiration = C6H12O6 + 6O2 → 6H2O 6 + CO2 ● Photosynthesis = 6H2O + 6CO2 → C6H12O6 + 6O2 ● Humans are diploidy two sets of chromosomes ○ Triploidy will have 3 sets of two (3 copies of chromosome 1, 3 copies of chromosome 2) ● What's the difference between an operon and a promoter? ○ Promoter is found in DNA, it is a binding site for RNA polymerase ■ Downstream from the promoter are genes for transcription ○ Operon cluster of genes to be transcribed together, a repressor can bind to it in and inhibit transcription. ■ Promoter → operon → G1 → G2 → G3 ● mRNA with a string of multiple start codons ● p53 suppressor protein normally functions to slow down or arrest the cell cycle (preventing cell division). Binds to DNA enhancer and acts as an activator to promote transcription of genes that are involved in DNA damage repair, cell cycle arrest, apoptosis. ○ If your p53 is mutated you won’t have the ability to fight mutations which could lead to cancer. ● What are the functions of the untranslated regions of the 5’/3’? THEY ARE INVOLVED IN REGULATING TRANSLATION (all we need to know) ○ mRNA (5’ UTR 3’ UTR) ■ 5’ region uORFs create short peptides, and can influence if the region is decoded. ■ 5 prime cap and the 3 prime polypeptide tail ○ Prok can just transcribe ■ mRNA ○ Euk will have splicing as well as the addition of the cap/tail ■ premRNA, mRNA, premiRNA, miRNA, tRNA, rRNA ● READ ABOUT RNA INTERFERENCE ● tRNA transfer RNA amino acids at one end with the anticodon at the other that is related to a particular codon. ● rRNA ribosomal RNA Ribosomes are made up of rRNAs and proteins, has a large and small subunit, rRNA catalyzes a reaction at the peptide bonds. ● Translation in bacteria ○ mRNA → small subunit with e binding sites E/P/A (tRNA comes in at the P site) → then the large subunit comes in and binds on top → then there is elongation ○ Elongation - only complimentary will bind to the condons, then there will be peptide bond formations which is catalyzed by rRNA between the amino acids 1 & 2. The attachment is broken at the P site and the only attached site with be the A site. → ribosomal translocation: the ribosome will shift over one triplet towards the 3’ end, which changes the attached site to P allowing for another tRNA to come in and repeat the process. → translocation: occurs when the tRNA leaves and is recharged by the enzyme aminoacyl-tRNA synthetases More Bio 160 review session notes ● promoter, where RNA polymerase binds (in eukaryotes) ● prokaryotes, RNA polymerase binds to sigma ● promoter is upstream of the gene for transcription ● operon= cluster of genes to be transcribed (G1, G2, G3) o also includes promoter and operator ● repressor binds to operator to inhibit transcription from occurring ● tumor suppressor gene P53 (post translational modification) o prevents cell division o binds to DNA o acts as a activator; promotes transcription o Activator= damage repair, promotes cell cycle arrest, promotes genes involved in apoptosis o Activators bind to repressors ● proto onco? gene promotes cell division ● Cell has to halt functioning when DNA/cell is affected by UV light RNA processing ● 5’ cap and 3’ poly a tail to make mature mRNA o 5’ sequenced in front of start codon and after stop codon o splicing of the introns= mature mRNA premRNA= only in eukaryotes (5’ à 3’) before cap and tail RNA interference ● pre mi RNA= double stranded hairpin loop ● micro RNA (mi RNA)= involved in regulating gene expression o segment of transcribed DNA that produces o RISC finds complementary target mRNA, RISC cuts mRNA in half=degradation ● tRNA translating the RNA into amino acid sequence o brings in the amino acid related to a particular codon o binds to ????? ● rRNA (ribosomal RNA) made of rRNA and proteins o ribosomes (proteins& rRNA) o rRNA catalyze the peptide bond formation at ribosome active site Translation initiation ● EPA is small subunit of ribosome = 3 binding sights for tRNA site E, P & A Aarrivial site P peptide bond formation E exit site ● tRNA binds to EPA Elongation ● Bunch of tRNA in cytoplasm, only complementary tRNA actually bind to EPA ● Transferred the growing polypeptide to tRNA in A site ● rRNA catalyzes peptide bond formation between amino acids (that will be protein) ● Amino acid bond breaks off from tRNA ● Ribosomal Translocation ribosome shifts one spot on mRNA, towards 3’ end ● EX) A> P, P> E ● ^^steps repeated, new tRNA come in
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